During embryonic development, dynamic remodeling of the chromatin landscape is required for the transcriptional machinery to access the genomic DNA in a spatiotemporally controlled manner. This intricate level of regulation allows precise gene regulation, necessary for complex morphogenetic processes. The Brg1/Brm-associated factor (BAF) complex is a multisubunit, ATP-dependent chromatin remodeling complex. Among the subunits, Brg1 is an ATPase that is critical for the function of the complex. Here, we study the role of Brg1 in foregut and cardiac outflow tract development. In the foregut, Brg1 functions with HDAC proteins in the ventral epithelium to regulate Nkx2-1 expression, essential for foregut septation into trachea and esophagus. In the absence of Brg1, embryos develop a single-tube foregut, reminiscent of human patients with tracheoesophageal fistula. In the developing heart, Brg1 functions in the secondary heart field-derived myocardium to control Semaphorin 3c (Sema3c) expression, essential for the outflow tract to septate into pulmonary artery and aorta. Deletion of Brg1 in the secondary heart field results in decreased neural crest cell colonization of the outflow tract, leading to a phenotype similar to the persistent truncus arteriosus pathology. Brg1 cooperates with HDAC proteins and Chd7 in the outflow tract myocardium to control Sema3c expression. These studies demonstrate novel functions and molecular mechanisms of Brg1 in foregut and cardiovascular development.

The medical specialty of pathology is focused on the transformation of information extracted from patient tissue samples into biologically informative and clinically useful diagnoses to guide research and clinical care. Since the mid-19th century, the primary data type used by surgical pathologists has been microscopic images of hematoxylin and eosin stained tissue sections. Over the past several decades, molecular data have been increasingly incorporated into pathological diagnoses. There is now a need for the development of new computational methods to systematically model and integrate these complex data to support the development of data-driven diagnostics for pathology. The overall goal of this dissertation is to develop and apply methods in this new field of Computational Pathology, which is aimed at: 1) The extraction of comprehensive integrated sets of data characterizing disease from a patient's tissue sample; and 2) The application of machine learning-based methods to inform the interpretation of a patient's disease state. The dissertation is centered on three projects, aimed at the development and application of methods in Computational Pathology for the analysis of three primary data types used in cancer diagnostics: 1) morphology; 2) biomarker expression; and 3) genomic signatures. First, we developed the Computational Pathologist (C-Path) system for the quantitative analysis of cancer morphology from microscopic images. We used the system to build a microscopic image-based prognostic model in breast cancer. The C-Path prognostic model outperformed competing approaches and uncovered the prognostic significance of several novel characteristics of breast cancer morphology. Second, to systematically evaluate the biological informativeness and clinical utility of the two most commonly used protein biomarkers (estrogen receptor (ER) and progesterone receptor (PR)) in breast cancer diagnostics, we performed an integrative analysis over publically available expression profiling data, clinical data, and immunohistochemistry data collected from over 4,000 breast cancer patients, extracted from 20 published studies. We validated our findings on an independent integrated breast cancer dataset from over 2,000 breast cancer patients in the Nurses' Health Study. Our analyses demonstrated that the ER-/PR+ disease subtype is rare and non-reproducible. Further, in our genomewide study we identified hundreds of biomarkers more informative than PR for the stratification of both ER+ and ER- disease. Third, we developed a new computational method, Significance Analysis of Prognostic Signatures (SAPS), for the identification of robust prognostic signatures from clinically annotated Omics data. We applied SAPS to publically available clinically annotated gene expression data obtained from over 3,800 breast cancer patients from 19 published studies and over 1,700 ovarian cancer patients from 11 published studies. Using these two large meta-datasets, we applied SAPS and performed the largest analysis of subtype-specific prognostic pathways ever performed in breast or ovarian cancer. Our analyses led to the identification of a core set of prognostic biological signatures in breast and ovarian cancer and their molecular subtypes. Further, the SAPS method should be generally useful for future studies aimed at the identification of biologically informative and clinically useful signatures from clinically annotated Omics data. Taken together, these studies provide new insights into the biological factors driving cancer progression, and our methods and models will support the continuing development of the field of Computational Pathology.

The placenta plays a fundamental role supporting pregnancy in all mammals, but exhibits unexpected and striking morphological and physiological variation across species. The rapid evolutionary diversification of the mammalian placenta is hypothesized to be a product of recurrent genetic conflict between parent and offspring. In this work, I investigate the genetic basis of rapid placenta evolution by using high-throughput genomic approaches, and address three major issues in placental biology. First, given that highly conserved genes govern placental development, the molecular mechanisms underlying the rapid diversification of placental morphology have remained unresolved. Our study reveals that the genome-wide regulatory landscape of placental development is highly divergent between closely related species, strongly implicating non-coding regulatory evolution as the major force driving placental morphological diversity. Second, endogenous retroviruses (ERVs) that are normally repressed throughout the embryo are rampantly expressed in the placenta, but the biological rationale--if any-- behind this apparent paradox has been unclear. We demonstrate that species-specific ERVs serve as a major source of functional enhancers during placental development, which provides a clear mechanism where placental ERV activity may facilitate the evolutionary diversification of placental morphology. Finally, our findings suggest a novel evolutionary model where placental ERVs provide an adaptive benefit under parent-offspring conflict. Given that genetic conflict predicts rapid diversifying evolution to maintain maximal fitness, we propose that placental ERVs act to dramatically increase the developmental evolvability of the placenta by serving as a rapidly evolving, epigenetically restricted source of polymorphic regulatory elements.

Nature has been evolving unparalleled molecular designs with extraordinary activity, simplicity, efficiency, and durability. The process of biomimicry takes inspiration from Nature. In this dissertation, I focused on the development of functional analogues of natural peptides and protein polymers for several applications that continue to challenge the biomedical field. Five applications were discussed: The first three sections focus on bioactive peptides that are generally shorter than 50 amino acids. The goal was to preserve the bioactivity of the natural peptides while reducing their natural sensitivity to proteases and fast in vivo clearance. The last two sections focus on developing protein polymer-based hydrogels. The goal was to generate biomimicking scaffolds for tissue regenerations. (i) Poly-N-substituted glycines, or peptoids, provide a biostable scaffold that can display a great diversity of side chains in highly tunable sequences via facile solid-phase synthesis. Current chemotherapeutics in oncology are often limited by side effect profiles and selection for drug resistance. Herein, I present a library of anticancer peptoids that mimic the cationic, amphipathic structural features of host defense peptides and explore their structure-activity relationship, and killing mechanisms. Several peptoids were found with broad cytotoxicity against cancer cells as well as the ability to overcome multidrug resistance. An initial in vivo study with a primary, orthotopic human breast cancer xenotransplantation model demonstrated anticancer efficacy of one of the studied peptoids. (ii) Cell-penetrating peptides have found numerous applications in biology and medicine as molecular transporters. We developed a library of cationic, amphipathic peptoids as a novel class of transporters and investigated the relationships between their structures, cellular uptake efficiency, and the associated cytotoxicity. Both guanidinium heads and bulky, aromatic hydrophobic residues were found to render the cationic, amphipathic constructs more permeable. Moreover, different internalization mechanisms were observed for peptoid transporters with distinct structures. One peptoid was identified as a promising transporter with excellent cellular uptake efficiency and low cytotoxicity. (iii) Bombesin (BBN) peptide can bind with high affinity and specificity to the GRP receptors (GRPR) which are upregulated invasive prostate cancer. BBN(7-14) provides a promising basis for developing radiometallated diagnostic or therapeutic radiopharmaceuticals to target GRPR positive prostate cancer. I report a design of a 4-arm PEG-based platform with multivalent BBN(7-14) for targeted delivery to the GRPR positive prostate cancer. The PEG-BBN conjugates displayed comparable tumor uptake as the free BBN while having both a lower liver uptake and higher tumor-to-blood ratio in a biodistribution study. (iv) Regenerative medicine is in need of bioactive extracellular matrix-like scaffolds that can interact with cells and allow tissue regeneration in a well-controlled manner. Via "controlled cloning", matrix metalloproteases (MMP) degradation sites were built into multiple sites along a protein polymer that can be enzymatically crosslinked into a previously established non-bioactive hydrogel systems. The incorporation of MMP degradation sites greatly improved cell infiltration into the hydrogel. (v) Lastly, a novel in situ forming hybrid, biomimetic hydrogel comprising bioactive recombinant protein polymers, hyaluronic acid (HA) and polyethylene glycol (PEG) was developed. In a preliminary study, this hydrogel was found to be biocompatible and bioactive, which opens up future studies with this hydrogel system.

Breast cancer is the second leading cause of female cancer death in the United States with an average lifetime risk of 1 in 8. Early detection of the disease and subsequent treatment increase the chance of survival. X-ray mammography is the standard imaging technique for breast cancer screening, but it is difficult to identify malignant lesions in women with dense breasts using x-ray mammography. Dynamic-contrast-enhanced (DCE) magnetic resonance imaging (MRI) has provided high sensitivity for breast cancer diagnosis due to its excellent soft tissue contrast, but there have been varied reports on its specificity. A recent study with a small surface coil has shown that high spatial and temporal resolution breast DCE MRI can improve sensitivity and specificity of ductal carcinoma in situ diagnosis by visualizing smaller scale features such as ductal and periductal enhancement. However, a small surface coil is not suitable for screening or bilateral staging exams where volumetric coverage of both breasts is necessary. Conversely, many commercially-available breast coils offer volumetric coverage of the breasts, but the large coil elements limit the signal-to- noise ratio (SNR) and thus the ability to increase spatial and temporal resolution with high parallel imaging acceleration factors. To address these concerns, we have designed and developed a custom-fitted 18-channel, bilateral breast radiofrequency (RF) coil array for providing high-resolution images in clinically-feasible scan times. The purpose of this work was three-fold: outline the construction process of a high- SNR custom-fitted array, benchmark its performance compared to a commercial design, and evaluate its utility for high-resolution clinical breast MRI. By placing a chain of overlapping small coil elements close to the tissue, we were able to obtain high SNR over the entire breast volume for medium-sized women. To reduce the overall exam time, we laid the coil elements in a geometry that facilitated bidirectional parallel imaging. Comparing the custom-fitted array to a commercially-available 8-channel breast array, the results show 3.6 times higher average SNR and superior parallel imaging quality for the custom-fitted array in volunteers. Using parallel imaging and taking advantage of the SNR benefits from the 18-channel coil array, we clinically demonstrated a 10-fold improvement in spatial resolution over the current Stanford Hospital protocol. We have conducted a clinical study comparing the diagnostic quality of high-resolution scans with the 18-channel array versus lower resolution scans in patients with suspicious lesions on mammography. The initial findings show that the improved resolution enables better depiction of overall lesion morphology and tissue interfaces. In summary, we have presented a method for constructing an 18-channel custom-fitted breast RF array and demonstrated its SNR and parallel imaging benefits. In a clinical setting, our initial findings show improved morphology characterization in high-resolution exams with the 18-channel array.

Genome Wide Association Studies (GWAS) have identified over 4,500 common variants in the human genome that are statistically associated with diseases and other phenotypical traits. Most identified associations, however, only have a small effect on disease risk, and their relevance in a clinical setting remains the subject of extensive debate. In this thesis I present three integrative analysis directions that extend on GWAS by developing new methods, by using genotyping data to ask new questions, and by integrating additional types of data to generate functional hypotheses about the biological processes underlying associations. First, I introduce a new classifier-based methodology that identifies similarities in the genetic architecture of diseases. This method can successfully identify both known and novel relationships between common diseases. Second, I show how control individuals from a GWAS can be used to detect genetic differences between the pseudoautosomal regions of chromosomes X and Y in the general population. Finally, I present an approach that integrates experimental data generated by the ENCODE consortium in order to identify functional Single Nucleotide Polymorphisms (SNPs). These functional SNPs are associated with a phenotype, either directly or through linkage disequilibrium, and overlap a functional region of the genome such as a transcribed region or a transcription factor binding site. Up to 80% of all associations previously reported in a GWAS can be mapped to a functional SNP.

There are clear physiological differences between men and women, including dimorphism in disease susceptibility and treatment response. These disparities often stem from biological differences between the sexes. Sex matters at every level of biology, including genes, proteins, pathways and tissues. Sex chromosomes are fundamental determinants of genetic makeup; sex hormones regulate the expression of thousands of genes; immune response pathways differ between the sexes; and clinical variables like heart rate and pain intensity are also divergent. With current technological advances in high-throughput measurement modalities, we can simultaneously probe every gene in the genome or record millions of clinical features in databases for research. However, investigators using large-scale data sources often ignore the question of sex differences. Many experimental studies use only male animals, and clinical trials often exclude one sex in an attempt to reduce variability in their results. This has led to many pharmaceuticals failing to receive approval by the Food and Drug Administration due to toxicity or lack of efficacy in the untested sex. Rather than completely ignoring sex or viewing it only as a variable to control for, we should make sex differences research a priority of every study. In particular, we should incorporate sex analysis into large-scale genomics, proteomics and clinical analyses. In addition, integrating different types of data will enable more powerful mechanistic studies. Investigating sex differences can lead to new insights about how disease operates differently in men and women. These insights will in turn lead us closer to the goal of personalized medicine for both men and women. In this thesis, I describe methods to address informatics challenges in performing sex-differentiated analysis of high-throughput datasets. In particular, I show that I have (1) developed a novel statistical method to systematically analyze genome-wide association study data for sex differences, (2) applied the method to discover and validate a novel sex difference in a top Crohn's disease risk gene, (3) developed methods to mine large electronic medical record databases to discover sex differences in clinical pain measures, and (4) modeled sex-specific gene-gene interactions to discover molecular sex differences in Alzheimer's disease. This dissertation contains a set of methods for (1) genomics and other data-driven researchers to discover sex differences in molecular and clinical measurements and (2) sex differences researchers to integrate large-scale data sources. Many of the methods I have developed are generalizable to any situation in disease or genomics research with a binary variable of interest.

This thesis encompasses three projects at the intersection of genetics, behavior, and neurobiology in the fruitfly, Drosophila melanogaster. The major work presented is an investigation of the afferent auditory system in D. melanogaster. The afferent auditory system of D. melanogaster arises from the Johnston's Organ in the second antennal segment, from which mechanosensory neurons project to a protocerebral region known as the Antennomechanosensory and Motor Complex (AMMC). The antennal mechanosensory system in Drosophila is used in multiple contexts, including vestibular mechanosensation, wind sensitivity, and courtship hearing. During courtship, male flies present a stereotypic pulse song as well as a hum-like sine-song to female flies; these stimuli are species-specific and critical to female receptivity. Using a large enhancer-Gal4 collection, I identify 12 candidate cell types within the AMMC, divided into 7 types of projection neurons as well as 5 types of local AMMC interneurons. I tested each of these cell types for its effect on courtship hearing by testing the effect of neuronal silencing on a) female receptivity, and b) a male locomotor response (Song-Induced Locomotion). These tests reveal that the activity of one class of projection neuron (aPN1), and one class of local interneuron (aLN(al)) are critical to courtship hearing in both male and female flies. Other cell types appear to be dispensable for courtship hearing, and may play a role in non-courtship related mechanosensation. To help confirm that these phenotypes are not specific to neuronal silencing, I also hyperactivated each cell type using the temperature-sensitive dTrpA1 reagent; these results confirm that aPN1 and aLN(al) alone are necessary for courtship hearing. Overall this work identifies a set of parallel pathways from the AMMC leading to the ventrolateral protocerebrum (VLPR), but reveal that only one of these pathways is necessary for courtship hearing. The structure of this circuit is analogous to the multi-lineage projection identified in D. melanogaster olfaction, in which a parallel pathways share a common projection but carry independent information. In addition to this work, I also discuss an investigation of the role of abnormal-chemosensory jump 6 (acj6) on escape behaviors, as well as an investigation of the expression of doublesex (dsx) in the nervous system.

Pancreatic [Beta]-cells secrete insulin to maintain systemic glucose balance. In response to physiological or pathological stresses that increase insulin demand, [Beta]-cells proliferate and enhance insulin secretion to increase insulin output. However, the mechanisms that govern these facultative changes are unclear. In this thesis, I investigate two potential factors in achieving these essential adaptive changes -- hypoxia inducible factor 1 alpha (Hif1a) and prolactin receptor (Prlr). During pregnancy, a common acquire state with increased insulin demand, Hif1a and Hif1a target gene expression, including Vegfa, Glut1, Gck were increased in maternal islets. Using mouse genetics, conditional deletion of Hif1a in [Beta]-cells ([Beta]Hif1a KO) resulted in glucose intolerance in pregnant, but not virgin, mice. Pregnant [Beta]Hif1a KO mice had impaired target gene expression, defective islet insulin secretion, and reduced vascularity. Pregnant mice develop transient hyperlipidemia, and recapitulation of the hyperlipidemia with fat-challenge or lipid treament induced Hif1a, Vegfa, and Pgk1 expression. Similar to pregnant [Beta]Hif1a KO mice, fat-challenged [Beta]Hif1a KO developed hyperglycemia, hypoinsulinemia, and glucose intolerance. All three hyperlipidemic states show ER stress, and treatment of unstressed mouse or human islets with thapsigargin was sufficient to increase Hif1a and downstream targets. To assess the significance of prolactin signaling in [Beta]-cell function and proliferation in adaptive settings, I created a novel conditional Prlr mouse model. In non-pregnant mice with [Beta]-cell-specific deletion of Prlr ([Beta]Prlr KO), glucose homeostasis is normal. However, pregnant [Beta]Prlr KO mice developed significant glucose intolerance. Given the widespread effects of lactogens on [Beta]-cell physiology, I anticipate altered [Beta]-cell proliferation and secretion in [Beta]Prlr KO islets, and current studies are underway to address this hypothesis. Collectively, our work has revealed that in settings of insulin resistance, both Hif1a and Prlr signaling play important roles in regulating the physiological changes required for proper [Beta]-cell function.

The overall goal of this dissertation is to use novel motion analysis systems to investigate the underlying mechanisms that cause an anterior cruciate ligament (ACL) injury and then to explore movement modification methods that might prevent ACL injuries from occurring. Additionally, novel motion analysis systems can provide new information about ACL injuries and therefore should be used to help analyze these injuries from a different perspective. This thesis provides the results from multiple experimental studies that used two novel motion analysis systems to investigate the underlying causes of ACL injury and potential injury prevention methods. Using a markerless motion capture system, the first investigation determined that increasing the coefficient of friction of the shoe-surface condition will change a subject's movement strategies during a sidestep cutting task in specific ways that may increase the risk of ACL injury. This investigation provides a biomechanical basis for the increased incidence of ACL injuries on high friction surfaces, and suggests that females are more at risk for ACL injury when cutting on high friction surfaces. In terms of novel motion analysis systems, there is a need for simple, cost effective methods to identify athletes at a higher risk for ACL injury during jumping tasks. As such, the second study assessed the capacity of a wearable inertial-based system to evaluate ACL injury risk during jumping tasks. The proposed system measured the knee flexion angle and the trunk lean, and demonstrated good concurrent validity and discriminative performance in terms of the known risk factors for ACL injury. This study also reported the angular velocity of the thigh and shank segments during bilateral and unilateral drop jumps for the first time. Furthermore, this study illustrated that there is an association between the coronal segment angular velocity and knee abduction moment, and that the coronal segment angular velocity can differentiate between subjects at higher risk for ACL injury. Recent studies have shown that the incidence of ACL injury can be decreased through the use of intervention programs. Therefore, the objective for the final study was to determine if an independent inertial-based system can be used to modify jump landing mechanics in order to decrease the risk for ACL injury by providing real-time feedback based on known kinematic and kinetic injury risk factors. This study found that the subjects reduced their risk for ACL injury after training with the system because there were significant increases in the maximum knee flexion angle and the maximum trunk lean. The subjects also reduced their risk for injury by decreasing their thigh coronal angular velocity, which was correlated with a decrease in their knee abduction moment. This study suggests that an inertial-based system could be used for interventional training aimed at reducing the risk for ACL injury.

In this dissertation, I investigate when and why gender segregation occurs in the professions of medicine, law and teaching. Drawing on social psychological perspectives on gender and theories on career development, I posit that segregation patterns differ across these three occupational contexts due to differences in gender valence of jobs and structures of career process. Specifically, I argue that early career choices are more gender-segregated in the highly gendered context of medicine and teaching, while the extent of gender segregation may vary (and increase) more substantially over time in the less structured contexts of teaching and law. Using data from professional organizations and government sources, I analyzed careers of a cohort of doctors, lawyers and teachers from their entry into their professions in 1991-1994 to 10-17 years after entry. Consistent with my hypotheses, doctors and teachers displayed highly gender-different aspirations than lawyers, and whereas the level of gender segregation remained fairly constant for doctors, it fluctuated somewhat for teachers and increased substantially for lawyers, particularly after the first six years of work. Analysis of 39 in-depth interviews further suggests that job choices among doctors and teachers reflect deeply held gendered ideas about people and work, whereas job choices among lawyers are seen as series of adjustments to organizational contexts, adjustments that usually differ for women and men. In total, these findings make the case for a more detailed view of intra-occupational gender segregation, one that places gender processes within the occupational context. In proposing a context-driven paradigm for studying gender inequality, this study brings the occupation to the center of the investigation, and argues for a more expansive view of gender segregation that takes into account the meanings and structures that delineate career decision-making and the constraints on the process.

In response to changing environments, the brains of vertebrates generate diverse behaviors change their morphology and physiology. Expression of genes in the brain is regulated by light, food, social stresses, and by internal signals including reproductive cycles and metabolism. To understand how these signals can have impact behaviors and the brain, I have studied regulation of reproduction, feeding, and light detection in a cichlid fish, Astatotilapia burtoni, and a circadian rhythm generation in the Siberian hamster, Phodopus sungorus. My experimentals involved measurement of mRNA by in situ hybridization and quantitative reverse transcription-PCR (qRT-PCR). To understand circadian rhythm entrainment, I studied when and where genes involved in circadian light detection are expressed in A. burtoni. mRNA encoding melanopsin, vertebrate ancient opsin, and pituitary adenylate cyclase-activating peptide were found in the inner retina of A. burtoni as well as in the brain. Their locations reveal a network homologous to circadian detection networks in other vertebrates. Melanopsin mRNA levels changed based on light input, as seen for some other opsin genes. Brief light stimuli can suppress circadian rhythms in several species. A two-pulse light treatment induces circadian arrhythmia in locomotor activity in P. sungorus. Loss of circadian rhythmicity in tissues and organisms could occur either through loss of intracellular rhythms or through loss of intercellular synchrony. Following the light treatment, P. sungorus had suppressed levels of mRNA encoding the core clock genes per1, per2, bmal1, and cry1 in the suprachiasmatic nucleus (SCN). Thus, circadian rhythm loss due to light stimuli involves inhibition of intracellular rhythms in the SCN. The brain controls reproductive behavior and physiology in response to relevant external and internal cues. Gonadotropin-releasing hormone (GnRH1) activates the reproductive system and GnRH1 peptide and mRNA levels are higher in dominant male A. burtoni than in subordinate males. Kisspeptin, a neuropeptide acting via the kisspeptin receptor (Kiss1r), increases GnRH1 release. In A. burtoni, I found kiss1r mRNA in GnRH1 and GnRH3 neurons and in many brain nuclei and kiss1r levels were higher in dominant males than in subordinate males. Kisspeptin signaling may regulate many brain functions, including responses to social status. Reproduction requires significant investment of metabolic energy, especially when parents provide care for offspring. Female A. burtoni carry eggs in their mouths for two weeks after spawning, during which time they do not eat. Food deprivation can affect reproductive and feeding behaviors and neuropeptides. To test the hypothesis that food deprivation and reproduction interact in regulating A. burtoni brain gene expression, I measured levels of several neuropeptide and receptor gene mRNAs following mouthbrooding or starvation. Mouthbrooding females had lower levels of gnrh1 mRNA than gravid females, but higher levels of cck and hcrt. In males, food deprivation decreased gnrh1 levels, but increased gnrh2, suggesting a novel feeding role for GnRH2 in fish. Mouthbrooding may inhibit reproduction and modulate feeding neural circuits. I also developed a technique for intracerebroventricular injections in A. burtoni that should facilitate manipulation of neuropeptide receptors including GnRH receptors. Matching behavior and physiology to accommodate changing lighting, social, feeding, and reproductive influences is important for maximizing organismal fitness and I have discovered how these factors regulate several genes that may contribute to adaptive responses in changing environments.

The concept of a personal genome stems from the fact that every human genome is unique. Measuring the unique features of a personal genome would help uncover the genetic basis of diseases and traits, and would be increasingly important in clinical diagnosis especially with the growing emphasis on personalized medicine. This thesis focuses on exploring the power of molecular counting to develop novel strategies that address the inadequacy of existing technologies in measuring the unique features of a human genome. The first focus of the thesis is aneuploidy detection, which has major application in prenatal diagnosis. While karyotyping of fetal cells is well-established for detecting aneuploidy, invasive sampling of fetal materials impose a small but significant risk to the health of both the mother and the fetus. A major research focus in the field of prenatal diagnosis has been to develop a noninvasive test for detecting fetal aneuploidy. Here, the concept of single molecule counting was applied to the problem of aneuploidy detection. The concept was first tested with digital PCR on invasively collected fetal materials, and subsequently extended to the noninvasive setting by shotgun sequencing maternal plasma DNA, which contains a small amount of fetal DNA. The former work led to the development of a polymorphism-independent method for rapid invasive diagnosis of aneuploidy, while the later work marked the development of the first polymorphism-independent method for the noninvasive diagnosis of fetal aneuploidy documented in the literature. The second focus of the thesis is molecular haplotyping. Present sequencing and other molecular techniques concentrate at identifying variants at isolated locations throughout a genome but largely ignore the haplotypes formed by these variants. Direct experimental determination of the haplotypes of an individual is challenging because of the lack of techniques to separate the two highly similar homologous copies of a chromosome. Here, a whole-genome haplotyping method was devised by analyzing amplified materials from single intact chromosomes within single cells, made possible by microfluidics. Such strategy enabled, for the first time, completely deterministic measurement of personal whole-genome haplotypes. It sets the stage for the direct sequencing of the two unique haploid genomes of any individual human, which has not been achieved by any personal genomes sequenced to date, and can potentially facilitate noninvasive fetal genome sequencing.

This dissertation explored expression of anger in the workplace through two experiments that varied in terms of the gender of the person expressing the anger, the frequency of the anger, and the object of the anger. Subjects reviewed resumes and performance reviews that they were told belonged to two consultants competing for the same promotion. Consultants who were said to express anger frequently were less likely to be promoted than neutral consultants. They also suffered social consequences, like being rated as less pleasant. Consultants who expressed anger a single time suffered social consequences (albeit less severe than those experienced by the frequently angry individuals) compared to neutral consultants, but their promotional outcomes were less affected. When respondents were given the option to promote both the neutral consultant and the angry consultant, most subjects chose to do so. The Study 1 results were based on an undirected expression of anger; Study 2 respondents were told that the anger was directed at a subordinate. A single instance of directed anger was more damaging to social and promotional outcomes than a single instance of undirected anger. Few gender effects were observed in either study, and the gender effects that were observed tended to favor females.

Emerging adulthood represents a critical phase for the development of purpose in life, yet little is known about the process through which young people become purposeful, or what the lasting benefits of such purposefulness might be. The present investigation explored four primary hypotheses though three interconnected studies. The first hypothesis, addressed in Study 1 using cross-sectional data, posited that purpose and meaningful engagement would be associated with psychological well-being. The second hypothesis proposed a mediational model, wherein the relationship between meaningful engagement and psychological well-being would be mediated by purpose; this hypothesis was tested first with cross-sectional data in Study 1 and again using longitudinal data in Study 2. Third, a moderation hypothesis was tested on the temporal relationship between purpose and psychological well-being, specifically that the relationship would be stronger for those high in self-transcendent life goals. Finally, Study 3 tested an intervention hypothesis to see whether engaging in deep reflection on and discussion about one's life goals can increase purpose and, consequently, psychological well-being. The results showed partial confirmation of the hypotheses. The cross-sectional analyses showed strong relations among meaningful engagement, purpose, and psychological well-being, and provided support for the proposed mediational model. However, the longitudinal analyses did not show significant relations among the constructs. The moderation hypothesis provided evidence that the path from purpose to well-being was stronger for those high on self-transcendent life goals, suggesting psychological benefits of pursuing purposes beyond oneself (but not self-oriented life goals). Finally, there was a significant positive effect of engaging in deep discussion and reflection on one's life goals, toward both increased purpose and increased psychological well-being. Implications of these findings for higher education in particular are discussed, and directions for future research are presented.